miv_simulator.plotting

Functions

clean_axes(axes[, left, right])	Remove top and right axes from pyplot axes object.
close_figure(fig)
get_RPSD(psd2D[, dTheta, rMin, rMax])
hex2rgb(hexcode)
init_spatial_rasters(ax, timebins, n_trials, ...)
plot_2D_histogram(hist, x_edges, y_edges[, ...])	type hist:
plot_2D_point_density(data[, width, height, ...])
plot_2D_rate_map(x, y, rate_map[, x0, y0, ...])	type x:
plot_biophys_cell_tree(env, biophys_cell[, ...])	Plot cell morphology and optionally synapse locations.
plot_cell_tree(population, gid, tree_dict[, ...])
plot_coordinates(coords_path, population, ...)	Plot coordinates
plot_coords_in_volume(populations, ...[, ...])
plot_graph(x, y, z, start_idx, end_idx[, ...])	Shows graph edges using Mayavi
plot_intracellular_state(input_path, ...[, ...])	Line plot of intracellular state variable (default: v).
plot_lfp(input_path[, config_path, ...])	Line plot of LFP state variable (default: v).
plot_lfp_spectrogram(input_path[, ...])	Line plot of LFP power spectrogram.
plot_network_clamp(input_path, ...[, ...])	Raster plot of target cell intracellular trace + spike raster of presynaptic inputs.
plot_single_vertex_dist(env, ...[, ...])	Plot vertex distribution with respect to arc distance for a single postsynaptic cell.
plot_spatial_bin_graph(graph_dict, **kwargs)
plot_spatial_spike_raster(input_path, ...[, ...])	Spatial raster plot of network spike times.
plot_spike_histogram(input_path, namespace_id)	Plots spike histogram.
plot_spike_raster(input_path, namespace_id)	Raster plot of network spike times.
save_figure(file_name_prefix[, fig])	type file_name_prefix:
show_figure()
update_spatial_rasters(frame, scts, ...)

miv_simulator.plotting.save_figure(file_name_prefix, fig=None, **kwargs)

Parameters:

• file_name_prefix –

• fig – :class:’plt.Figure’

• kwargs – dict

miv_simulator.plotting.plot_graph(x, y, z, start_idx, end_idx, edge_scalars=None, edge_color=None, **kwargs)

Shows graph edges using Mayavi

Parameters:

x: ndarray

x coordinates of the points

y: ndarray

y coordinates of the points

z: ndarray

z coordinates of the points

edge_scalars: ndarray, optional

optional data to give the color of the edges.

kwargs:

extra keyword arguments are passed to quiver3d.

miv_simulator.plotting.clean_axes(axes, left=True, right=False)

Remove top and right axes from pyplot axes object. :type axes: :param axes: list of pyplot.Axes :param top: bool :type left: :param left: bool :type right: :param right: bool

miv_simulator.plotting.plot_coordinates(coords_path, population, namespace, index=0, graph_type='scatter', bin_size=0.01, xyz=False, **kwargs)

Plot coordinates

Parameters:

• coords_path –

• namespace –

• population –

miv_simulator.plotting.plot_spike_raster(input_path, namespace_id, include=['eachPop'], time_range=None, time_variable='t', max_spikes=1000000, labels='legend', pop_rates=True, spike_hist=None, spike_hist_bin=5, include_artificial=True, marker='.', **kwargs)

Raster plot of network spike times. Returns the figure handle.

input_path: file with spike data namespace_id: attribute namespace for spike events time_range ([start:stop]): Time range of spikes shown; if None shows all (default: None) time_variable: Name of variable containing spike times (default: ‘t’) max_spikes (int): maximum number of spikes that will be plotted (default: 1e6) labels = (‘legend’, ‘overlay’): Show population labels in a legend or overlayed on one side of raster (default: ‘legend’) pop_rates = (True|False): Include population rates (default: False) spike_hist (None|’overlay’|’subplot’): overlay line over raster showing spike histogram (spikes/bin) (default: False) spike_hist_bin (int): Size of bin in ms to use for histogram (default: 5) marker (char): Marker for each spike (default: ‘|’)

miv_simulator.plotting.plot_spike_histogram(input_path, namespace_id, config_path=None, include=['eachPop'], time_variable='t', time_range=None, pop_rates=False, bin_size=5, smooth=0, quantity='rate', include_artificial=True, progress=False, overlay=True, graph_type='bar', **kwargs)

Plots spike histogram. Returns figure handle.

Parameters:

input_pathstr

file with spike data

namespace_id

attribute namespace for spike events

config_pathOptional[str]

config_path

includeList[str] ([“eachPop”, <population name>])

List of data series to include. (default: [“eachPop”] expands to the name of each population)

time_variablestr

Name of variable containing spike times (default: “t”)

time_rangeOptional[Tuple[int,int]] ([start:stop])

Time range of spikes shown. If None shows all. (default: None)

pop_ratesbool

pop_rates

bin_sizeint

Size in ms of each bin (default: 5)

smoothfloat

smooth

quantitystr (“rate”, “count”)

Quantity of y axis (firing rate in Hz, or spike count) (default: “rate”)

include_artificialbool

include_artificial

progressbool

progress

overlaybool

Whether to overlay the data lines or plot in separate subplots (default: True)

graph_typestr (“line”, “bar”)

Type of graph to use (line graph or bar plot) (default: “line”)

miv_simulator.plotting.plot_lfp(input_path, config_path=None, time_range=None, compute_psd=False, window_size=4096, frequency_range=(0, 400.0), overlap=0.9, bandpass_filter=False, dt=None, **kwargs)

Line plot of LFP state variable (default: v). Returns figure handle.

config: path to model configuration file input_path: file with LFP trace data time_range ([start:stop]): Time range of spikes shown; if None shows all (default: None)

miv_simulator.plotting.plot_lfp_spectrogram(input_path, config_path=None, time_range=None, window_size=4096, overlap=0.9, frequency_range=(0, 400.0), dt=None, **kwargs)

Line plot of LFP power spectrogram. Returns figure handle.

config: path to model configuration file input_path: file with LFP trace data time_range ([start:stop]): Time range of spikes shown; if None shows all (default: None)

miv_simulator.plotting.plot_biophys_cell_tree(env, biophys_cell, node_filters={'swc_types': ['apical', 'basal']}, plot_synapses=False, synapse_filters=None, syn_source_threshold=0.0, line_width=8.0, plot_method='neuron', **kwargs)

Plot cell morphology and optionally synapse locations.

miv_simulator.plotting.plot_2D_rate_map(x, y, rate_map, x0=None, y0=None, peak_rate=None, title=None, fft_vmax=10.0, density_bin_size=10.0, **kwargs)

Parameters:

• x – array

• y – array

• rate_map – array

• peak_rate – float

• title – str

miv_simulator.plotting.plot_2D_histogram(hist, x_edges, y_edges, norm=None, ylabel=None, xlabel=None, title=None, cbar_label=None, cbar=True, vmin=0.0, vmax=None, **kwargs)

Parameters:

• hist – ndarray

• x_edges – ndarray

• y_edges – ndarray

• norm – ndarray; optionally normalize hist by nonzero elements of norm array

• ylabel – str

• xlabel – str

• title – str

• cbar_label – str

• cbar – bool

• vmin – float

• vmax – float

miv_simulator.plotting.plot_intracellular_state(input_path, namespace_ids, include=['eachPop'], time_range=None, time_variable='t', state_variable='v', max_units=1, gid_set=None, n_trials=1, labels='legend', lowpass_plot=None, reduce=False, distance=False, **kwargs)

Line plot of intracellular state variable (default: v). Returns the figure handle.

input_path: file with state data namespace_ids: attribute namespaces time_range ([start:stop]): Time range of spikes shown; if None shows all (default: None) time_variable: Name of variable containing spike times (default: ‘t’) state_variable: Name of state variable (default: ‘v’) max_units (int): maximum number of units from each population that will be plotted (default: 1) labels = (‘legend’, ‘overlay’): Show population labels in a legend or overlayed on one side of raster (default: ‘legend’)

miv_simulator.plotting.plot_network_clamp(input_path, spike_namespace, intracellular_namespace, gid, target_input_features_path=None, target_input_features_namespace=None, target_input_features_arena_id=None, target_input_features_trajectory_id=None, config_file=None, config_prefix='', include='eachPop', include_artificial=True, time_range=None, time_variable='t', intracellular_variable='v', labels='overlay', pop_rates=True, all_spike_hist=False, spike_hist_bin=5, lowpass_plot_type='overlay', n_trials=-1, marker='.', opt_seed=None, **kwargs)

Raster plot of target cell intracellular trace + spike raster of presynaptic inputs. Returns the figure handle.

input_path: file with spike data spike_namespace: attribute namespace for spike events intracellular_namespace: attribute namespace for intracellular trace target_input_features_path: optional file with input features target_input_features_namespaces: optional attribute namespace for input features config_path: path to network configuration file; required when target_input_features_path is given time_range ([start:stop]): Time range of spikes shown; if None shows all (default: None) time_variable: Name of variable containing spike times (default: ‘t’) labels = (‘legend’, ‘overlay’): Show population labels in a legend or overlayed on one side of raster (default: ‘legend’) pop_rates = (True|False): Include population rates (default: False) spike_hist_bin (int): Size of bin in ms to use for histogram (default: 5) marker (char): Marker for each spike (default: ‘.’)

miv_simulator.plotting.plot_single_vertex_dist(env, connectivity_path, coords_path, distances_namespace, target_gid, destination, source, extent_type='local', direction='in', bin_size=20.0, normed=False, comm=None, **kwargs)

Plot vertex distribution with respect to arc distance for a single postsynaptic cell.

Parameters:

• env –

• connectivity_path –

• coords_path –

• distances_namespace –

• target_gid –

• destination –

• source –

miv_simulator.plotting.plot_spatial_spike_raster(input_path, namespace_id, coords_path, distances_namespace='Arc Distances', include=['eachPop'], time_step=5.0, time_range=None, time_variable='t', include_artificial=True, max_spikes=1000000, marker='o', **kwargs)

Spatial raster plot of network spike times. Returns the figure handle.

input_path: file with spike data namespace_id: attribute namespace for spike events time_range ([start:stop]): Time range of spikes shown; if None shows all (default: None) time_variable: Name of variable containing spike times (default: ‘t’) max_spikes (int): maximum number of spikes that will be plotted (default: 1e6) labels = (‘legend’, ‘overlay’): Show population labels in a legend or overlayed on one side of raster (default: ‘legend’) marker (char): Marker for each spike (default: ‘|’)